mbSet<-Init.mbSetObj()
mbSet<-SetModuleType(mbSet, "mdp")
mbSet<-ReadSampleTable(mbSet, "metadata 6-Yes and No.txt");
mbSet<-Read16STaxaTable(mbSet, "taxonomy_19.01.txt");
mbSet<-Read16SAbundData(mbSet, "ASV-feature-table_19.01.txt","text","Others/Not_specific","T","false");
mbSet<-SanityCheckData(mbSet, "text","sample","true");
mbSet<-SanityCheckSampleData(mbSet);
mbSet<-SetMetaAttributes(mbSet, "1")
mbSet<-PlotLibSizeView(mbSet, "norm_libsizes_0","png");
mbSet<-SanityCheckData(mbSet, "text","none","false");
mbSet<-SanityCheckSampleData(mbSet);
mbSet<-SetMetaAttributes(mbSet, "1")
mbSet<-PlotLibSizeView(mbSet, "norm_libsizes_1","png");
mbSet<-CreatePhyloseqObj(mbSet, "text","Others/Not_specific","F" , "false")
smpl.nm.vec <- c("RS001.V1","RS002.V1","RS003.V1","RS005.V1","RS006.V1","RS007.V1","RS008.V1","RS009.V1","RS010.V1","RS011.V1","RS012.V1","RS013.V1","RS014.V1","RS015.V1","RS016.V1","RS017.V1","RS018.V1","RS019.V1","RS020.V1","RS021.V1","RS022.V1","RS023.V1","RS024.V1","RS025.V1","RS026.V1","RS027.V1","RS028.V1","RS029.V1","RS030.V1","RS031.V1","RS032.V1","RS033.V1","RS034.V1","RS035.V1","RS036.V1","RS037.V1","RS038.V1","RS039.V1","RS040.V1","RS042.V1","RS043.V1","RS044.V1","RS046.V1","RS048.V1","RS049.V1","RS050.V1","RS051.V1","RS052.V1","RS053.V1")
mbSet<-UpdateSampleItems(mbSet);
smpl.nm.vec <- c("RS001.V1","RS002.V1","RS003.V1","RS005.V1","RS006.V1","RS007.V1","RS008.V1","RS009.V1","RS010.V1","RS011.V1","RS012.V1","RS013.V1","RS014.V1","RS015.V1","RS016.V1","RS017.V1","RS018.V1","RS019.V1","RS020.V1","RS021.V1","RS022.V1","RS023.V1","RS024.V1","RS025.V1","RS026.V1","RS027.V1","RS028.V1","RS029.V1","RS030.V1","RS031.V1","RS032.V1","RS033.V1","RS034.V1","RS035.V1","RS036.V1","RS037.V1","RS038.V1","RS039.V1","RS040.V1","RS042.V1","RS043.V1","RS044.V1","RS046.V1","RS048.V1","RS049.V1","RS050.V1","RS051.V1","RS052.V1","RS053.V1")
mbSet<-UpdateSampleItems(mbSet);
mbSet<-ApplyAbundanceFilter(mbSet, "prevalence", 0, 0.1);
mbSet<-ApplyVarianceFilter(mbSet, "iqr", 0.0);
mbSet<-GetLibscale(mbSet);
mbSet<-PerformNormalization(mbSet, "none", "none", "none", "true",4142);
mbSet<-PerformBetaDiversity(mbSet, "beta_diver_0","PCoA","bray","expfac","type","none","OTU","","Chao1", "yes", "adonis", "png", 72, "default", "true");
mbSet<-PerformBetaDiversity(mbSet, "beta_diver_1","PCoA","bray","expfac","type","none","OTU","","Chao1", "yes", "adonis", "png", 72, "default", "true");
mbSet<-PCoA3D.Anal(mbSet, "PCoA","bray","OTU","expfac","type","","Chao1","beta_diver3d_0.json")
mbSet<-PCoA3D.Anal(mbSet, "PCoA","bray","OTU","expfac","type","","Chao1","beta_diver3d_1.json")
mbSet<-PerformCategoryComp(mbSet, "OTU", "adonis","bray","type","true");
mbSet<-PerformCategoryComp(mbSet, "OTU", "adonis","bray","type","true");
mbSet<-PlotAlphaData(mbSet, "filt","alpha_diver_0","Chao1","type","OTU", "default", "png");
mbSet<-PlotAlphaBoxData(mbSet, "alpha_diverbox_0","Chao1","type","default", "png");
mbSet<-PerformAlphaDiversityComp(mbSet, "tt","type","true");
mbSet<-PlotAlphaData(mbSet, "filt","alpha_diver_1","Chao1","type","OTU", "default", "png");
mbSet<-PlotAlphaBoxData(mbSet, "alpha_diverbox_1","Chao1","type","default", "png");
mbSet<-PerformAlphaDiversityComp(mbSet, "nonpar","type","true");
mbSet<-PlotAlphaData(mbSet, "filt","alpha_diver_2","Observed","type","OTU", "default", "png");
mbSet<-PlotAlphaBoxData(mbSet, "alpha_diverbox_2","Observed","type","default", "png");
mbSet<-PerformAlphaDiversityComp(mbSet, "nonpar","type","true");
mbSet<-PlotAlphaData(mbSet, "filt","alpha_diver_3","Shannon","type","OTU", "default", "png");
mbSet<-PlotAlphaBoxData(mbSet, "alpha_diverbox_3","Shannon","type","default", "png");
mbSet<-PerformAlphaDiversityComp(mbSet, "nonpar","type","true");
mbSet<-PlotTaxaAundanceBar(mbSet, "taxa_alpha_0","Phylum","type", "null", "barraw",10, "set3","sum",10, "bottom", "F", "png");
mbSet<-PlotTaxaAbundanceBarSamGrp(mbSet, "taxa_alpha_1","Phylum","type", "none", "barraw",10,"set3","sum", 10, "top", "F", "png");
mbSet<-PlotTaxaAbundanceBarSamGrp(mbSet, "taxa_alpha_2","Phylum","type", "none", "barnorm",10,"set3","sum", 10, "top", "F", "png");
mbSet<-PrepareHeatTreePlot(mbSet, "type", "Genus", "dbgr", "reda", "No_vs_Yes", 0.05, "false", "all", "true", "heat_tree_0","png");
mbSet<-PerformRNAseqDE(mbSet, "EdgeR",0.05,"type","NA","OTU",0.0, "null1", "null2");
mbSet<-PerformRNAseqDE(mbSet, "EdgeR",0.05,"type","NA","OTU",0.0, "null1", "null2");
mbSet<-GenerateCompJson(mbSet, "comp_graphics_0.json","png" ,"EdgeR",1,"OTU", "Phylum",0.05);
mbSet<-GenerateCompJson(mbSet, "comp_graphics_1.json","png" ,"EdgeR",1,"OTU", "Phylum",0.05);
mbSet<-PerformRNAseqDE(mbSet, "EdgeR",0.05,"type","NA","Genus",0.0, "Yes", "No");
mbSet<-GenerateCompJson(mbSet, "comp_graphics_2.json","png" ,"EdgeR",1,"Genus", "Phylum",0.05);
mbSet<-PerformRNAseqDE(mbSet, "EdgeR",0.05,"type","NA","Species",0.0, "Yes", "No");
mbSet<-GenerateCompJson(mbSet, "comp_graphics_3.json","png" ,"EdgeR",1,"Species", "Phylum",0.05);
smpl.nm.vec <- c("RS001.V1","RS002.V1","RS003.V1","RS005.V1","RS006.V1","RS007.V1","RS008.V1","RS009.V1","RS010.V1","RS011.V1","RS012.V1","RS013.V1","RS014.V1","RS015.V1","RS016.V1","RS017.V1","RS018.V1","RS019.V1","RS020.V1","RS021.V1","RS022.V1","RS023.V1","RS024.V1","RS025.V1","RS026.V1","RS027.V1","RS028.V1","RS029.V1","RS030.V1","RS031.V1","RS032.V1","RS033.V1","RS034.V1","RS035.V1","RS036.V1","RS037.V1","RS038.V1","RS039.V1","RS040.V1","RS042.V1","RS043.V1","RS044.V1","RS046.V1","RS048.V1","RS049.V1","RS050.V1","RS051.V1","RS052.V1","RS053.V1","RS001.AT","RS002.AT","RS003.AT","RS005.AT","RS007.AT","RS008.AT","RS009.AT","RS010.AT","RS011.AT","RS012.AT","RS013.AT","RS014.AT","RS015.AT","RS016.AT","RS017.AT","RS019.AT","RS020.AT","RS021.AT","RS022.AT","RS023.AT","RS024.AT","RS025.AT","RS026.AT","RS027.AT","RS028.AT","RS029.AT","RS030.AT","RS031.AT","RS032.AT","RS033.AT","RS035.AT","RS036.AT","RS037.AT","RS038.AT","RS039.AT","RS040.AT","RS042.AT","RS043.AT","RS044.AT","RS045.AT","RS046.AT","RS048.AT","RS049.AT","RS050.AT","RS051.AT","RS052.AT","RS053.AT")
mbSet<-UpdateSampleItems(mbSet);
mbSet<-ApplyAbundanceFilter(mbSet, "prevalence", 0, 0.1);
mbSet<-ApplyVarianceFilter(mbSet, "iqr", 0.0);
mbSet<-GetLibscale(mbSet);
mbSet<-PerformNormalization(mbSet, "none", "none", "none", "true",1427);
mbSet<-PlotHeatmap(mbSet, "heatmap_0", "norm", "row","euclidean","ward.D","bwm","type","OTU","heatmap","F", "png","T","T",23,10,12,6, 2.0,10.0,"F","F","NA");
mbSet<-PlotHeatmap(mbSet, "heatmap_1", "norm", "row","euclidean","ward.D","bwm","type","OTU","heatmap","F", "png","T","T",23,10,12,6, 2.0,10.0,"F","F","NA");
mbSet<-PlotHeatmap(mbSet, "heatmap_2", "raw", "row","euclidean","ward.D","bwm","subtype","Phylum","heatmap","F", "png","T","T",23,10,12,6, 2.0,10.0,"F","F","type");
mbSet<-PlotHeatmap(mbSet, "heatmap_3", "raw", "row","euclidean","ward.D","bwm","subtype","Phylum","heatmap","T", "png","T","T",23,10,12,6, 2.0,10.0,"F","F","type");
mbSet<-PlotHeatmap(mbSet, "heatmap_4", "raw", "row","euclidean","ward.D","bwm","type","Phylum","heatmap","F", "png","T","T",23,10,12,6, 2.0,10.0,"F","F","type");
mbSet<-PlotHeatmap(mbSet, "heatmap_5", "raw", "row","euclidean","ward.D","bwm","type","Phylum","heatmap","F", "png","F","T",23,10,12,6, 2.0,10.0,"F","F","type");
mbSet<-PlotHeatmap(mbSet, "heatmap_6", "raw", "row","euclidean","ward.D","bwm","subtype","Phylum","heatmap","F", "png","F","T",23,10,12,6, 2.0,10.0,"F","F","type");
